Microarray analysis provides a means by which the abundances of many thousands of transcripts can be followed simultaneously as genes respond to experimental or physiological cues. When experiments are more focused on a smaller number of genes that have been selected either by preliminary microarray analysis or by other means, standard microarrays become a cumbersome tool for further characterization. In the R21 phase, a novel microarray method is developed that would allow individual genes to be analyzed over many thousands of experimental conditions. The method is based on the development of low complexity representations of the mRNA of the cell. These low complexity representations are then spotted on a glass slide to produce a 'vertical' microarray, which can be probed with single fluorescently labeled probes. The low complexity representations are employed to increase signal. Multiple low complexity representations are used in order to include most of the complexity of the original mRNA population. Thousands of experimental variables can be explored on a single array, one gene at a time, or a few genes at a time using multi-color fluorescence. In the R33 phase, the vertical array method will be used to characterize the detailed responses of genes known to be controlled by a particular transcription factor to a collection of drugs and hormones. This data will be used to construct a class predictor that predicts whether or not a particular transcription factor is likely to be involved in the regulation of a gene.